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Series GSE71171 Query DataSets for GSE71171
Status Public on Aug 22, 2016
Title Broad and largely overlapping molecular changes arise in thymic and peripheral XCR1+ dendritic cells upon tolerogenic and immunogenic maturation
Organism Mus musculus
Experiment type Expression profiling by array
Third-party reanalysis
Summary This SuperSeries is composed of the SubSeries listed below.
 
Overall design DC were isolated from lymphoid organs as previously described (Vremec et al., 2000). DC subsets were sorted by flow cytometry according to the marker combinations described in the 'characteristics: phenotype' field for each sample for each individual series.

GeneChip Mouse Gene 1.0 ST (GPL6246) and GeneChip Mouse Genome 430 2.0 (GPL1261) DAT files were processed using Affymetrix Gene Chip Operating System to generate .CEL files. Normalization of the raw Affymetrix expression data with Robust Multi-chip Analysis were performed through Bioconductor in the R statistical environment (version 3.0.2) using the oligo package (GPL6246) and the affy, affyPLM and yaqcaffy packages (GPL1261). For genes symbol with several probeSets, the most variant probSet has been selected. The two platforms where merged by the unique genes symbols. Quantile Normalization was applied on the merged expression arrays to generate Matrix 1. PCA analysis revealed a strong platform effect. Partial Least Square (PLS) was performed to remove the platform effect and yield Matrix2 which was used for subsequent analyses. The data matrices contain log2 values.
 
Citation(s) 27533013
Submission date Jul 21, 2015
Last update date Mar 04, 2019
Contact name Marc DALOD
E-mail dalod@ciml.univ-mrs.fr
Organization name CIML
Street address Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9
City MARSEILLE
ZIP/Postal code 13009
Country France
 
Platforms (2)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
Samples (67)
GSM1828776 im_T_XCR1+_CCR7-_1
GSM1828777 im_T_XCR1+_CCR7-_2
GSM1828778 im_T_XCR1+_CCR7-_3
This SuperSeries is composed of the following SubSeries:
GSE71166 Thymic XCR1+ dendritic cells undergo a functional maturation fundamentally similar to that of peripheral tolerogenic XCR1+ dendritic cells
GSE71167 A fraction of steady state splenic XCR1+ dendritic cells undergo an homeostatic maturation as assessed by their upregulation of CCR7 or of IL-12, and by their profound genetic reprogramming
GSE71168 Gene expression profiling of mouse spleen XCR1+ DC at steady state, 3 hours after polyI:C or 12 hours after STAg i.v. injection
Relations
BioProject PRJNA290486

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71171_RAW.tar 253.9 Mb (http)(custom) TAR (of CEL)
GSE71171_matrix1_quantilenormalization_allsamples.txt.gz 6.0 Mb (ftp)(http) TXT
GSE71171_matrix2_partialleastsquare_allsamples.txt.gz 6.8 Mb (ftp)(http) TXT

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